User Tools

Site Tools



This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
lecture_notes:03-30-2011 [2011/03/31 20:45]
svohr [Pac Bio]
lecture_notes:03-30-2011 [2011/04/01 12:20] (current)
svohr [Coverage] slight corrections
Line 25: Line 25:
   * Cheaper than SoLiD, 10K Genomes project uses it.   * Cheaper than SoLiD, 10K Genomes project uses it.
 ==== Ion Torrent ==== ==== Ion Torrent ====
 +  * 2x100 base pairs 
 +  * ~50,000 to 5,000,000 reads depending on Sequencing Chip [(cite:​ionTorrent>​http://​​technology-how-does-it-perform/​)]. 
 +  * Ion semiconductor sequencing. No optics or modified bases are required.
 ==== Pac Bio ==== ==== Pac Bio ====
   * Very long, single molecule reads (~10K)   * Very long, single molecule reads (~10K)
   * High error rates (~5%)   * High error rates (~5%)
   * Useful when mapping to a reference.   * Useful when mapping to a reference.
 +===== Coverage =====
 +We briefly discussed how much sequence data would be required to assemble the genome. First, we considered the probability of seeing a particular base ''​i''​ in a single read ''​j''​.
 +  ​
 +  P( seeing base i in read j ) = L/G
 +where ''​L''​ is the read length and ''​G''​ is the total size of the genome. If we have ''​R''​ reads, then 
 +  P( never seeing base i ) = (1 - L/G)^R
 +We can multiply ''​L/​G''​ by ''​R/​R''​ to get ''​((L*R) / G) / R''​ or ''​C / R''​ where ''​C''​ is our coverage of the genome. We take the limit of this as
 +''​R''​ goes to infinity:
 +  lim n->inf (1 - C/R)^R = e^-C
 +Thus we can expect to miss ''​G*e^-C''​ bases.
 +We cannot assemble an entire chromosome if we are missing bases. However, we can construct contiguous stretches of bases or //contigs// and later
 +assemble them into //​scaffolds//​ using other information,​ such as long distance physical maps.
 ===== References ===== ===== References =====
 <​refnotes>​notes-separator:​ none</​refnotes>​ <​refnotes>​notes-separator:​ none</​refnotes>​
 ~~REFNOTES cite~~ ~~REFNOTES cite~~
lecture_notes/03-30-2011.1301629550.txt.gz · Last modified: 2011/03/31 20:45 by svohr